PLUMED-NEST

Project ID: plumID:23.044
Source: plumed_files/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

full: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-60
The GROUP action with label full calculates somethingcpp: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=198-297
The GROUP action with label cpp calculates somethingc1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=full 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=cpp 
R_0
The r_0 parameter of the switching function
=0.25 
The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the value of the coordination
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
 
ARG
the input for this action is the scalar output from one or more other actions
=c1
 
HEIGHT
the heights of the Gaussian hills
=2
 
PACE
the frequency for hill addition
=20000
 
SIGMA
the widths of the Gaussian hills
=0.5
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
 
GRID_MIN
the lower bounds for the grid
=0
 
GRID_MAX
the upper bounds for the grid
=100
 
GRID_BIN
the number of bins for the grid
=400
 
FILE
 a file in which the list of added hills is stored
=HILLS
 
ACCELERATION
 Set to TRUE if you want to compute the metadynamics acceleration factor
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.acc
the metadynamics acceleration factor
COMMITTOR
Does a committor analysis. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=c1
  
STRIDE
 the frequency with which the CVs are analyzed
=500
  
BASIN_LL1
List of lower limits for basin #
=-0.1
  
BASIN_UL1
List of upper limits for basin #
=0.1
... COMMITTOR

The COMMITTOR action with label  calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=c1,metad 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=500